The prior design approaches for fringe projection autofocus systems irradiate wafer and reference surfaces with the same grating and illumination angle for all wavelength bands. Some such systems are described in Smith et al., U.S. patent application Ser. No. 13/066,741, Smith et al., U.S. Patent Application Publication 2011/0071784, Goodwin et al., U.S. Provisional Patent Application 61/575,330, Goodwin et al., U.S. Patent Application Publication 2010/0245829, Goodwin et al., U.S. Provisional Patent Application 61/500,521, and Goodwin et al., U.S. Provisional Patent Application 61/647,324, all of which are incorporated herein by reference. In such systems all wavelength bands have nominally the same sensitivity to wafer height changes. In these systems, optical path differences (OPDs) such as those due to thermal/pressure changes in air are wavelength dependent. Because errors due to air turbulence are different for different wavelength bands, height measurements and focus correction are difficult.